Differential methylation calling suite for Nanopore methylation calls PycoMeth
Project description
Version in this branch: 2.2.1
DNA methylation analysis downstream to Nanopolish for Oxford Nanopore DNA sequencing datasets
pycoMeth can be used for further analyses starting from the output files generated by Nanopolish call-methylation. The package contains a suite of tools to find CpG islands, segment methylome, and to perform a differential methylation analysis across multiple samples.
pycoMeth generates extensive tabulated reports and BED files which can be loaded in a genome browser. In addition, an interactive HTML report of differentially
methylated intervals/islands can also generated at the end of the analysis.
Methplotlib developed by Wouter de coster is an excellent complementary tool to visualise and explore methylation status for specific loci.
Please be aware that pycoMeth is a research package that is still under development. The API, command line interface, and implementation might change without retro-compatibility.
Installation
Install either using conda:
conda install -c snajder-r -c bioconda pycometh
Or using pip:
pip install pycometh
pycoMeth workflow
pycoMeth example output IGV rendering
pycoMeth example HTML report
Citing
The repository is archived at Zenodo. If you use pycoMeth version 2, please cite as follow:
Rene Snajder. (2021, May 18). snajder-r/pycoMeth. Zenodo. https://doi.org/10.5281/zenodo.4772051
For version 1, please cite as:
Adrien Leger. (2020, January 28). a-slide/pycoMeth. Zenodo. https://doi.org/10.5281/zenodo.3629254
Authors and contributors
- Rene Snajder (@snajder-r): rene.snajder@dkfz-heidelberg.de
- Adrien Ledger (@a-slide)
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